From: Ivana (stankoviciv_at_gmail.com)
Date: Mon Jul 08 2013 - 11:22:36 CDT
The standard error output contains accepted exchanges: replica number,
temperature, replica number, temperature, run number ( for example
EXCHANGE_ACCEPT 9 (412.21) 10 (427.34) RUN 7)
You can save it to an output file by commenting the line in the
replica.namd file:
# puts stderr "EXCHANGE_ACCEPT $rid ($temp) $rid2 ($temp2) RUN $i_run"
and adding the lines:
set acceptance_file [open $output/acceptance.dat a ]
puts $acceptance_file "EXCHANGE_ACCEPT $rid ($temp) $rid2 ($temp2) RUN
$i_run"
close $acceptance_file
and then calculate the percentage:
numrepl=18
input=outputREMD/acceptance.dat
total=`grep RUN $input | tee matches.txt | wc -l `
rm matches.txt
sum=0
for (( i=1; $i <= $numrepl ; i=$i+1 )) ; do
accepted=`grep $i $input | tee matches.txt | wc -l `
rm matches.txt
sum=$(($sum+$accepted))
done
acceptance_ratio=`echo "($sum / (($numrepl * $total))*100)" | bc -l`
echo "acceptance_ratio=" $acceptance_ratio "%"
Regards, Ivana
On 8 July 2013 12:23, Martin, Erik W <Erik.Martin_at_stjude.org> wrote:
>
> I've tried searching with no success… I'm wondering what the individual
> columns of the .history file that's written in a replica exchange
> simulation are. The first seems to be step, second the replica, third the
> temperature… the fourth I'm confused on.
>
> Also, I'd like a simple way to calculate from these files the percentage
> of successful exchanges I get. Is there an easy way to do this?
>
> Thanks,
> Erik
>
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